Examples with Parameter dr.inference.model.Parameter used on opensource projects

Example 56 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class TreeClusterAlgorithmOperator method Propose_changeMuAndBalance.

private double Propose_changeMuAndBalance() {
    //System.out.println("root: " + mu.getParameter(0).getParameterValue(0) + "," + mu.getParameter(0).getParameterValue(1));
    //for(int i=0; i < numNodes; i++){
    //	if( (int) indicators.getParameterValue(i) == 1){
    //		System.out.println(i + ": " + mu.getParameter(i+1).getParameterValue(0) + "," + mu.getParameter(i+1).getParameterValue(1));
    //	}
    //}
    //first, randomly select an "on" node to overwrite
    //find an on-node	
    int originalNode = findAnOnNodeIncludingRootRandomly();
    //originalNode = 673;
    //if(originalNode == 802){
    //System.out.println(treeModel.getRoot().getNumber());
    //System.out.println("I am walking 802!");
    //}
    //unbounded walk
    int dimSelect = (int) Math.floor(Math.random() * 2);
    double change = Math.random() * WALK_SIZE - WALK_SIZE / 2;
    //dimSelect = 0;
    //change = 10;	
    //double originalValue = mu.getParameter(originalNode +1).getParameterValue(dimSelect);
    double originalValue = mu.getParameter(originalNode).getParameterValue(dimSelect);
    //System.out.println("originalValue = " + originalValue);
    mu.getParameter(originalNode).setParameterValue(dimSelect, originalValue + change);
    //mu.getParameter(originalNode + 1).setParameterValue(dimSelect, originalValue + change);
    //System.out.println("original node = " + originalNode);
    //a. by removing the selected node, each child of this node should be updated to keep the absolute location of 
    //the child cluster fixed as before
    LinkedList<Integer> childrenOriginalNode = findActiveBreakpointsChildren(originalNode);
    //}
    for (int i = 0; i < childrenOriginalNode.size(); i++) {
        //int muIndexNum = childrenOriginalNode.get(i).intValue() + 1;
        int muIndexNum = childrenOriginalNode.get(i).intValue();
        //if(originalNode == 802){
        //System.out.println(" " + muIndexNum + " is a child");
        //}
        Parameter curMu = mu.getParameter(muIndexNum);
        double curMu_original = curMu.getParameterValue(dimSelect);
        mu.getParameter(muIndexNum).setParameterValue(dimSelect, curMu_original - change);
    //System.out.println( " " + ( muIndexNum - 1) + " is a child");
    }
    return (0);
}

Example 57 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class RandomWalkOnActiveMu method doOperation.

public double doOperation() {
    //first, randomly select an "on" node to overwrite
    //find an on-node	
    int originalNode = Tree_Clustering_Shared_Routines.findAnOnNodeIncludingRootRandomly(numNodes, indicators);
    //unbounded walk
    int dimSelect = (int) Math.floor(Math.random() * 2);
    double change = (2.0 * MathUtils.nextDouble() - 1.0) * windowSize;
    double originalValue = mu.getParameter(originalNode).getParameterValue(dimSelect);
    mu.getParameter(originalNode).setParameterValue(dimSelect, originalValue + change);
    //a. by removing the selected node, each child of this node should be updated to keep the absolute location of 
    //the child cluster fixed as before
    LinkedList<Integer> childrenOriginalNode = Tree_Clustering_Shared_Routines.findActiveBreakpointsChildren(originalNode, numNodes, treeModel, indicators);
    for (int i = 0; i < childrenOriginalNode.size(); i++) {
        int muIndexNum = childrenOriginalNode.get(i).intValue();
        Parameter curMu = mu.getParameter(muIndexNum);
        double curMu_original = curMu.getParameterValue(dimSelect);
        mu.getParameter(muIndexNum).setParameterValue(dimSelect, curMu_original - change);
    }
    //the virus location needs to be updated because the mu's are updated 	  				
    Tree_Clustering_Shared_Routines.updateUndriftedVirusLocations(numNodes, numdata, treeModel, virusLocationsTreeNode, indicators, mu, virusLocations, correspondingTreeIndexForVirus);
    return 0.0;
}

Example 58 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class TreeClusterAlgorithmOperator method Proposal_flipIBalance.

private double Proposal_flipIBalance() {
    //System.out.println("hi it got run");
    //System.exit(0);
    //System.out.println("root: " + mu.getParameter(0).getParameterValue(0) + "," + mu.getParameter(0).getParameterValue(1));
    //for(int i=0; i < numNodes; i++){
    //if( (int) indicators.getParameterValue(i) == 1){
    //System.out.println(i + ": " + mu.getParameter(i+1).getParameterValue(0) + "," + mu.getParameter(i+1).getParameterValue(1));
    //}
    //}
    int node = findNodeRandomly();
    //int node = (int) (Math.floor(Math.random()*numNodes));
    //node = 785;
    //System.out.println("selected node " + node);
    //double[] originalValues = mu.getParameter(node +1).getParameterValues();	
    double[] originalValues = mu.getParameter(node).getParameterValues();
    //System.out.println(originalValues[0] + " and " + originalValues[1]);
    //a. by turning on the selected node, each child of this node should be updated to keep the absolute location of 
    //the child cluster fixed as before
    LinkedList<Integer> childrenOriginalNode = findActiveBreakpointsChildren(node);
    if ((int) indicators.getParameterValue(node) == 0) {
        indicators.setParameterValue(node, 1);
        for (int i = 0; i < childrenOriginalNode.size(); i++) {
            int muIndexNum = childrenOriginalNode.get(i).intValue();
            //int muIndexNum = childrenOriginalNode.get(i).intValue() + 1;
            Parameter curMu = mu.getParameter(muIndexNum);
            double curMu_original0 = curMu.getParameterValue(0);
            mu.getParameter(muIndexNum).setParameterValue(0, curMu_original0 - originalValues[0]);
            double curMu_original1 = curMu.getParameterValue(1);
            mu.getParameter(muIndexNum).setParameterValue(1, curMu_original1 - originalValues[1]);
        //System.out.println( " " + ( muIndexNum - 1) + " is a child");
        }
    } else {
        indicators.setParameterValue(node, 0);
        //System.out.println("turn it off");
        for (int i = 0; i < childrenOriginalNode.size(); i++) {
            int muIndexNum = childrenOriginalNode.get(i).intValue();
            //int muIndexNum = childrenOriginalNode.get(i).intValue() + 1;
            Parameter curMu = mu.getParameter(muIndexNum);
            double curMu_original0 = curMu.getParameterValue(0);
            mu.getParameter(muIndexNum).setParameterValue(0, curMu_original0 + originalValues[0]);
            double curMu_original1 = curMu.getParameterValue(1);
            mu.getParameter(muIndexNum).setParameterValue(1, curMu_original1 + originalValues[1]);
        //System.out.println( " " + ( muIndexNum - 1) + " is a child");
        }
    }
    double coord1 = mu1Scale.getParameterValue(0) * originalValues[0];
    double coord2 = mu2Scale.getParameterValue(0) * originalValues[1];
    muDistance = Math.sqrt(coord1 * coord1 + coord2 * coord2);
    return (0);
}

Example 59 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class TreeClusterAlgorithmOperator method Propose_branchOffFlip.

private double Propose_branchOffFlip() {
    //first, randomly select an "on" node to overwrite
    //find an on-node	
    int originalNode = findAnOnNodeRandomly();
    //second, randomly select a destination
    //sample a node that's not in the cluster.
    int site_add = findAnOffNodeRandomly();
    //existing mu
    Parameter selectedMu = mu.getParameter(originalNode);
    //Parameter selectedMu = mu.getParameter(originalNode +1) ;
    double selectedMu0 = selectedMu.getParameterValue(0);
    double selectedMu1 = selectedMu.getParameterValue(1);
    //a. by removing the selected node, each child of this node should be updated to keep the absolute location of 
    //the child cluster fixed as before
    LinkedList<Integer> childrenOriginalNode = findActiveBreakpointsChildren(originalNode);
    for (int i = 0; i < childrenOriginalNode.size(); i++) {
        int muIndexNum = childrenOriginalNode.get(i).intValue();
        //int muIndexNum = childrenOriginalNode.get(i).intValue() + 1;
        Parameter curMu = mu.getParameter(muIndexNum);
        double mu0 = curMu.getParameterValue(0) + selectedMu0;
        double mu1 = curMu.getParameterValue(1) + selectedMu1;
        mu.getParameter(muIndexNum).setParameterValue(0, mu0);
        mu.getParameter(muIndexNum).setParameterValue(1, mu1);
    }
    //set indicators AND NEW MU
    indicators.setParameterValue(site_add, 1);
    //indicators.setParameterValue(originalNode, 0); //just flip it on. do not replace
    //I think this generate a situation where if a mu walks off, then it gets the breakpoint that doesn't partition.
    //this creates a scenario where a breakpoint is lost
    //double change = Math.random()*WALK_SIZE - WALK_SIZE ; 
    //double newMu0 = selectedMu0 + change;
    //double change2 = Math.random()*WALK_SIZE- WALK_SIZE ; 
    //double newMu1 = selectedMu1 + change2;
    double[] oldValues = mu.getParameter(site_add).getParameterValues();
    //double[] oldValues = mu.getParameter(site_add+1).getParameterValues();
    //System.out.println(oldValues[0]  + ", " + oldValues[1]);
    //instead, sample from the normal distribution
    double[] mean = new double[2];
    mean[0] = 0;
    mean[1] = 0;
    double[][] precisionM = new double[2][2];
    //double precision = 1/TreeClusterViruses.getSigmaSq();
    double precision = muPrecision.getParameterValue(0);
    precisionM[0][0] = precision;
    precisionM[0][1] = 0;
    precisionM[1][0] = 0;
    precisionM[1][1] = precision;
    double[] values = MultivariateNormalDistribution.nextMultivariateNormalPrecision(mean, precisionM);
    //System.out.println(values[0]  + ", " + values[1]); 
    mu.getParameter(site_add).setParameterValue(0, values[0]);
    mu.getParameter(site_add).setParameterValue(1, values[1]);
    //mu.getParameter(site_add+1).setParameterValue(0,values[0]);
    //mu.getParameter(site_add+1).setParameterValue(1,values[1]);
    selectedMu.setParameterValue(0, values[0]);
    selectedMu.setParameterValue(1, values[1]);
    //b. by adding the new selected node, each child of this new node should be updated to keep the absolute location of 
    //the child cluster fixed as before
    LinkedList<Integer> childrenNewNode = findActiveBreakpointsChildren(site_add);
    for (int i = 0; i < childrenNewNode.size(); i++) {
        //int muIndexNum = childrenNewNode.get(i).intValue() + 1;
        int muIndexNum = childrenNewNode.get(i).intValue();
        Parameter curMu = mu.getParameter(muIndexNum);
        double mu0 = curMu.getParameterValue(0) - values[0];
        double mu1 = curMu.getParameterValue(1) - values[1];
        mu.getParameter(muIndexNum).setParameterValue(0, mu0);
        mu.getParameter(muIndexNum).setParameterValue(1, mu1);
    }
    double logHastingRatio = MultivariateNormalDistribution.logPdf(oldValues, mean, precision, 1) - MultivariateNormalDistribution.logPdf(values, mean, precision, 1);
    return (logHastingRatio);
}

Example 60 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class TreeClusterAlgorithmOperator method PrintsetMembershipTreeToVirusIndexes.

/*
	private void setMembershipTreeToVirusIndexes(){

  	   //I suspect this is an expensive operation, so I don't want to do it many times,
  	   //which is also unnecessary  - MAY have to update whenever a different tree is used.
         correspondingTreeIndexForVirus = new int[numdata]; 
         for(int i=0; i < numdata; i++){
  		   Parameter v = virusLocations.getParameter(i);
  		   String curName = v.getParameterName();
  		  // System.out.println(curName);
  		   int isFound = 0;
      	   for(int j=0; j < numNodes; j++){
      		   String treeId = treeModel.getTaxonId(j);
      		   if(curName.equals(treeId) ){
      		//	   System.out.println("  isFound at j=" + j);
      			   correspondingTreeIndexForVirus[i] = j;
      			   isFound=1;
      			   break;
      		   }	   
      	   }
      	   if(isFound ==0){
      		   System.out.println("not found. Exit now.");
      		   System.exit(0);
      	   }     	   
         }
    }
*/
private void PrintsetMembershipTreeToVirusIndexes() {
    //I suspect this is an expensive operation, so I don't want to do it many times,
    //which is also unnecessary  - MAY have to update whenever a different tree is used.
    correspondingTreeIndexForVirus = new int[numdata];
    for (int i = 0; i < numdata; i++) {
        Parameter v = virusLocations.getParameter(i);
        String curName = v.getParameterName();
        System.out.print(curName);
        int isFound = 0;
        for (int j = 0; j < numNodes; j++) {
            String treeId = treeModel.getTaxonId(j);
            if (curName.equals(treeId)) {
                System.out.print("  isFound at j=" + j);
                correspondingTreeIndexForVirus[i] = j;
                System.out.println(" has clusterLabel = " + clusterLabelsTreeNode.getParameterValue(j));
                isFound = 1;
                break;
            }
        }
        if (isFound == 0) {
            System.out.println("not found. Exit now.");
            System.exit(0);
        }
    }
}